The Wellington Phoenix will continue to fight for their right to sign All White Michael McGlinchey, despite an independent arbitrator ruling against them today.

Following months of legal wrangling, arbitrator Peter Kite today determined that McGlinchey remained contracted to the Central Coast Mariners despite a change of ownership at the A-League club last year.

The Phoenix had been confident that the arbitrator, employed by Football Federation Australia, would rule in their favour and the accomplished midfielder would be allowed to join his hometown club.

The confusion stems from a change of ownership at the Mariners last year.

McGlinchey had been contracted to Central Coast for the 2014-15 A-League season but the Mariners chose to re-write existing player contracts as part of the ownership change.

At the time, McGlinchey was playing on loan in Japan for Vegalta Sendai and he declined to sign a new contract with the Mariners - in his view therefore making him a free agent and able to sign with the Phoenix.

But Kite has ruled differently.

McGlinchey has been training with the Phoenix for months and has told Central Coast coach Phil Moss that he does not want to play for him.

The 27-year-old has the backing of Professional Footballers Australia, who argue McGlinchey has the right to sign for the Phoenix.

''The Phoenix will now wait to see the result of the PFA's appeal into this decision,'' Phoenix general manager David Dome told Fairfax Media tonight.

''We'll take our own legal advice as well. We still firmly believe Michael McGlinchey has the right to sign for us but we obviously have to follow the due legal process.

''We're supporting him as best we can but there's no doubt that Michael is disappointed. The club is rallying around him and I think it's fair to say that the club has come together over the issue and is quite determined to follow it through right to the end.''

Dome said McGlinchey planned to keep training with the Phoenix.

''He's a valuable player and we can understand the Mariners' desire to keep hold of him,'' Dome said.

''We've acted in good faith and I guess Central Coast have done the same. Now it is up to the FFA to clarify the licence status of the Mariners so this issue can be resolved. We're going to try our hardest to keep Michael McGlinchey at the club. We really want him here, he really wants to be here, we think we're in the right position.''

PFA chief executive Adam Vivian said the FFA had advised them in October last year that the Mariners' licence would be transferred to a new company controlled by owner Mike Charlesworth.

Under an agreement between FFA and the PFA, that meant all Mariners players were to be offered employment with the new company, and the previous Mariners' entity would cease to operate the A-League licence.

''As a result, almost the entire Mariners squad has signed agreements with the new entity,'' Vivian said.

''As Michael was contracted to the previous entity, he was free to pursue his professional interests as an uncontracted player and sign a contract with a club of his choice. However, it only recently emerged that the entity licensed to operate the Mariners had not changed, but will do so in the near future.

''The reason for the failure to transfer the licence has not been satisfactorily explained to the PFA.''

Vivian said the PFA was greatly concerned by the Mariners situation and the sanctity of the A-League licensing system, claiming that players had previously lost over A$2.5 million in entitlements when a new entity refused to pick up contracts on the transfer of an A-League licence.